How to run PWM scan with hundreds of PWM at the same time?

Question

[juanpjlozano]

Hi,

Is there a way to run PWMscan with several PWMs at the same time? I am trying to obtain BED files with the TFBS coordinates for the full CIS-BP D.melanogaster database (several hundred PWMs) and the PWMscan website only allows to run with one PWM at a time,

If you know any other way to obtain a list of these BED files, that works fine too. Doesn't have to be PWMscan,

Thank you so much!